In recent years, the increase in container ship sizes is progressing prominently due to the expansion of worldwide economy, accompanied by usage of materials of higher strength. These changes cause relatively smaller hull girder rigidity, posing concerns on the increased hull girder whipping response and its influence on the hull girder ultimate strength. Moreover, the increase in container ship sizes caused greater ship breadths and more flexible double bottom structure, which also affects the hull girder ultimate strength. In this paper, the authors investigated ‘influence of the hull girder flexibility to the whipping response’ and ‘the correlation factors between the double bottom bending and the hull girder bending’ in irregular waves through a combined numerical simulation method, comprising ship motion and wave load analysis based on Rankine source method and subsequent 3-dimensional whole ship finite element analysis based on Newmark-β method.